Open the System Configuration dialog from the main Clarity window and check the tab of the corresponding instrument Instrument x (1).

In the left-hand Setup Control Modules list select the correct detector ﻿﻿(2) connected to the A/D card you are using and assign it (﻿3) to the corresponding instrument (4) on the right.

If your A/D card is not in the left-hand Setup Control Modules list, add it using the Add button (5) and repeat the previous step.

Click on the OK button and return to the instrument window. Data acquisition window is now functional.

b) You have purchased a licence for data collection for a smaller number of instruments:

Open the System Configuration dialog from the main Clarity window using the System - Configuration command and check the tab of the corresponding instrument - Instrument x. If the symbol of the curve in the tab header is blue (6), it means that the instrument can not be used for data acquisition but only for method preparation and chromatogram evaluation.

Check your serial number S/N, using the Help - About command from the main Clarity window.

In case you want to measure on this instrument as well contact DataApex or your local distributor.

In case your PC and chromatograph is connected directly via LAN and autodetect is not possible, use the following configuration.

Note that you need cross-over ethernet cable (straight-through cable is not recommended).

Open Control Panel - Network and Internet - Network and Sharing Center - Change adapter settings - right mouse click on the Local Area Connection and choose Properties.

In the Local Area Connection Properties, choose item Internet Protocol Version 4 and click the Properties button.

In the Internet Protocol Version 4 (TCP/IPv4) Properties window change use the option to Use the following IP address.

Fill the IP address. The first three possitions define the network and must be the same as in the device IP address. The last position defines the device and must be unique within the network, so it must be set different from that of the connected instrument.

Eventually other Ethernet boards within the computer must not share the same network.

Most probably yes, the list contains only directly controlled autosamplers. In other words those where it is possible to set the position and injection method. Nevertheless Clarity enables basic synchronization (allow injection and start data acquisition) with arbitrary automsamplers equiped with appropriate control output (eventually input).

For more information read through the chapter on autosamplers - "AS - Passive Sequence (GC or LC)" in the Getting Started.

Clarity user must have read/write access to Clarity system and data files. The default C:Clarty directory inherits Read Only status from C: on administered systems. Contact your local administrator to change the settings.

Antivirus programs:

Antivirus programs usually do not interfere with Clarity functionality. But there are two areas which may pose problems for correct functioning of Clarity:

Antivirus is causing processor overload under certain situations which may leave insufficient memory resources for Clarity.

Antivirus is continuously monitoring files frequently updated by Clarity (.raw,.audit etc.) which may be unjustifiably marked as a threat to the PC.

Windows Updates:

Automatic Windows updates are in the default settings able to force unattended computer to restart regardles of running programs - only warning message will appear. Please note, the first two options (Automatic updates or Download updates) may result in the forced computer restart.

In Windows XP in the Control Panel - Automatic Updates choose one of the options:

Turn off Automatic Updates.

Notify me but don't automatically download or install them.

On administered systems ask your local administrator to choose on of the options described above.

Since Clarity version 6.0, DEMO is a standalone application. Functions of Clarity DEMO remain unchanged. To upgrade from DEMO to full version of Clarity, it is required to download full version from www.dataapex.com in the download section or obtain it from your local distributor.

Problem

The USB or LPT Hardware Key is not functional.

Symptoms

The "DEMO - missing HW keylock" inscription in the Clarity main window. Note that this is until Clarity 6.0.

Since Clarity version 6.0, Clarity will not enter into "Demo" mode. If Clarity loses connection with the HW key, user is presented with a dialog and has 5 min to try to resolve the situation. Once this time elapses Clarity will be forced to shut down.

Solution

Before you will do anything, ensure the corresponding port (USB, LPT) is enabled in the BIOS settings (integrated peripherals). The drivers can be install even if it is not enabled, however the key will not function then.

a) For a dongle connected to a parallel port check the following:

Try to print to the printer.

Ensure that the printing cable is not too long (>3m).

Disconnect the printer cable and connect the dongle directly to the port of the computer.

b) For a USB dongle, check the folowing:

See whether the USB port is working (e.g. try connecting different device and see if it's working etc.)

See whether the HW driver is installed. In such case the green LED on the dongle should be on.

Depending on type of Hardware Key you get with the Clarity, continue with the proper chapter. See images below:

Rockey USB ND

Rockey USB

Rockey LPT

Sentinel USB

Sentinel LPT

Rockey USB ND

Rockey USB ND does not need seperate installation of drivers. Drivers will be automaticaly installed once plugged into the USB port.

At first sight, Rockey USB ND is distinguished from other keys by the fact that the casing is grey and transparent (internal chip is visible).

If it will not help, please check, if the used USB port is functional or try to install the station on another computer.

Rockey LPT

1. Verify that the key is properly inserted in the LPT (printer) port. 2. In filemanager (e.g. Windows Explorer) navigate to C:CLARITYHW_DRIVERSROCKEY 3. Run the "InstDrv.exe" file to invoke Setup Wizard. 4. Select Repair in the first dialog and click Next. 5. In the second dialog check the Install parallel driver checkbox. 6. Select the Detect the parallel business radiobutton and click the Next button. 7. In the third dialog click the Complete button. 8. You will be asked to Restart Windows. If this will not help, then contact our technical support.

Further observed limitations of the LPT hardware key

Rockey LPT key does not function on LPT2 and higher, it can be used only with LPT1

Rockey will function only on onboard LPT ports and ignore the ports on PCI cards.

On one Clarity data station it is possible to configure and control up to 4 independent instruments (GC or HPLC). Only one Clarity station can run on one PC.

However please, consider such configuration may not be practical in cases when all 4 instruments should be running simultaneously with short analyses (less than 20 minutes) due to the following issues:

Method sending for some GC and HPLC systems is a lengthy operation and during this time Clarity may not be operable.

During chromatogram processing, after the end of acquisition the Clarity may again not respond for some time.

If there is more than one operator there may be struggle for keyboard control.

The demands for processing time/memory may exceed the available resources on weak computers.

Please note, there may be also specific limitations given by the controlled instrument (for example only one Agilent 1100 system using HP-IB communication or only one Shimadzu LC-10/20 system may be controlled on Clarity station) due to the communication protocol constraints.

Under normal circumstances drivers for the MultiCOM are installed without any problems when FULL installation of Clarity is performed. Nevertheless under MS Windows 8.1 drivers for the MultiCOM may not be installed properly. If that is the case you may be presented with the following error: "Windows found driver for your device but encountered an error while attempting to install it. The system cannot find the path specified."

There are two ways to rectify this situation:

Reinstall the drivers manually. The process is described in the Troubleshooting section in the MultiCOM manual. Link to the manual is here.

If the first solution does not work then the problem may be on the computer side. Possible way to solve this issue is to restore the system, perform updates and uninstall some of the ‘bonus’ (spyware, online help utilities, etc.) software. After that reinstall Clarity with FULL installation option and connect the MultiCom again.

The customer can connect up to 4 instruments (chromatographs) with the Clarity Chromatography Station on one PC. Up to 32 detectors (channels) on 1 instrument. PCs usually have 3-4 PCI slots. The user can also combine PCI A/D cards with the U-PAD/U-PAD2/Colibrick (USB) and Net-PAD converters.

Windows 8 and later may contain predefined larger size of font than in previous versions. It may occur also in Windows 7 when a user change the font size.

In case Clarity is displaying apparently larger font, cut text or labels in table headers, etc. - check the setting in Control Panel - Display. We recommend to set the Smaller - 100% (default) option, see the image below:

The "No Data received for 10 sec" or "No data from Acquisition..." messages mean what they say, no data were received from a detector or convertor (Colibrick, U-PAD2, etc.) for a certain period of time. It may be caused by several cases:

1) In most cases caused by some problem on the computer - processor overload, interference on the USB bus, time consuming net search or backup operations blocking the communication for some time. The error invoked will cause stopping an acquisition or interrupting of the sequence.

Suspected programs are incorrectly set antivirus (continuous checking of file types used by Clarity during data acquisition - raw, prm, audit, tmp should be avoided), programs monitoring files on exchangeable media (i.e. programs for organizing and presenting of pictures, music or video, including some CD/DVD burning programs). One such persisting problem was reportedly solved by removing the Roxio Burning software.

This will occur more frequently on slow computers, the triggering action may be processor overload or some programs blocking the communication for extended period.

Suspected programs are incorrectly set antivirus (continuous checking of file types used by Clarity during data acquisition - raw, prm, audit, tmp should be avoided), programs monitoring files on exchangeable media (i.e. programs for organizing and presenting of pictures, music or video, including some CD/DVD burning programs).

2) In some cases, Windows may suspend power of the USB HUB in the computer and this unexceptionally causes loss of connection to Colibrick or U-PAD2. Try to check the Device Manager dialog - Universal Serial Bus controllers. Display the Generic USB HUB Properties dialog - Power Management tab. Set Disabled for option Allow the computer to turn off this device to safe power.

If you installed Clarity 5.0.2.612, you may experience a stability issue when using a Knauer PDA detector. Also, the existing methods are not compatible with the driver in 5.0.2.612 and will display an error.

In case need to keep the installation of Clarity 5.0.2.612, please, download and install the provided hotfix, start Clarity and in the Instrument window, create new PDA method.

In case you you are able to update Clarity, please download and install Clarity 5.0.5 or later.

In Clarity version 5.0.0 - 5.0.2 it is not possible to set Use ISTD function in standard groups in the Calibration. It may cause an error when opening chromatograms which contains standard groups calculated by an internal standard.

This is fixed in Clarity 5.0.3, please download latest version from our Download center.

Windows 8 is fully supported from Clarity 4.0.4.987. Previous version of Clarity did not detect the new type of HW key (RkNDUSB, grey) properly. You can upgrade to the latest Clarity on our Download Center .

If you have an anti-virus software which scans your web communication and downloads for viruses, it may hangs the download in your web browser at the end of the download process. The length of the delay depends on the size of the file and it may appear in Firefox, Chrome, Internet Explorer, etc.

Clarity is save to download. Microsoft implemented new functions in the latest versions of Windows which warns the user when downloading a not commonly known application from the Internet. In the example described in the picture below, click the Actions buttons and select Run Anyway.

Since Clarity is specialized SW, it takes a time until Microsoft will trust the publisher (DataApex) and will stop displaying such a warning.

Yes, from Clarity version 4.0 it is possible to define the name of the file including the subdirectory, in both the Sequence window and the Single Analysis dialog - use the sign %s before the file name.

You can use the standard Clarity variables in the name of the subdirectory - the file name could look like in the example below:

In the example above, %s\%q_%Q_%R defines the file name: a subdirectory with the sequence name (%s) will be created in the working directory and in it, the files with the name format SampleID_Sample_Date-and-Time.The folder will be created at the start of the acquisition (you might be prompted for confirmation) or only the file if the subfolder already exists.

Please, do not break Windows file and folder naming rules - ie. check that the last character in the folder name is not a space etc.

RkUSB Dongle keys may not work properly on computers with "AMD USB Audio Driver Filter" installed. It is recommended to check the driver details of RkUSB in Device Manager. In case a "usbfilter.sys" is listed, uninstall "AMD USB Audio Driver Filter" driver from Windows using the "Add or Remove Programs" function in Windows. For more details, see support pages of your PC's manufacturer.

This problem is caused by HP ProtectTools suite, installed on most new Hewlett-Packard computers. The particular file responsible for this behavior is DPAgent.exe, purposed for controlling the fingerprint scanner. The easiest solution of the problem is to rename this file, thus it will be not automatically launched after startup of the computer. Standard location of the file is C:Program Files (x86)Hewlett-PackardHP ProtectTools Security ManagerBinDPAgent.exe, however it may differ slightly on different versions of the suite. For fixing the problem, the file has to be renamed (we recommend to rename it to DPAgent.bak.exe, thus it can be easily renamed back when necessary). In case you need to use the fingerprint scanner, it is also possible to terminate this file only when you intend to launch Clarity datastation. It can be made manually (using Task Manager) or facilitated by some utility able to kill a process running on the computer.

You can open the chromatogram on the Clarity Instrument which is in Offline mode. In Clarity - System Configuration, increase the Number of Instruments option in the top right part of the window. Even if you have license for one Clarity Instrument, you can use other Clarity Instruments without measuring data from detectors or controlling your instruments. This can be helpful for evaluating chromatograms without turning on the instruments in your lab or if you use the Clarity, for example, in your home - see FAQ about running Clarity on on multiple computers using 1 dongle (hw key).

At first check, if the U-PAD2 isn't connected to a USB hub. Problems are mostly related to the USB power supply, so definitely the hub should have external power source.

Note the U-PAD2 is sensitive to communication delays. Responsible for those delays on USB communication may be the computer hardware or software. Processor overload, low RAM memory or running processes blocking the processor or communication lines should be checked. In case the communication is interrupted for more then 10 seconds, an error will be invoked. Error message "No data from Acquisition", "No data received for ..." and similar may appear randomly. As a consequence, the running acquisition is stopped and the running sequence interrupted. In case the problem is temporary, sending of the method again may solve the problem.

Try the Task Manager and inspect the processor load and processes consuming large amount of CPU time or memory. Suspected programs are incorrectly set anti-virus (continuously checking file types used by Clarity during data acquisition. The *.raw, *.prm, *.audit, *.tmp file types should be avoided diabled for scans. Any other programs monitoring files on exchangeable media (i.e. programs for organizing and presenting of pictures, music or video, including some CD/DVD burning programs) may also interrupt the Acquisition.

Also, when the Acquisition is running, it may be interrupted by any actions started during this, like a printing to a slow USB or network printer, large file transfer over network or USB, connecting or disconnecting USB devices, computer entering sleep mode or screen-saver activation.

This problem is caused by the wrong configuration file saved when the computer was shut down while Clarity was running. Normally, Clarity saves data to its configuration file when exiting. When the computer is shut down while doing this, the clarity.cfg file may be corrupted and cannot be used in Clarity next time it is opened.

The corruption of the clarity.cfg file may happen in numerous ways - when the computer is switched of while the Clarity is running, while experiencing some fluctuations in the power system or, which seems to be the cause of your client according to the lunch time, when the computer is switched to the sleep mode while Clarity is open, but not running. While the analysis in Clarity is running, Clarity can block the switching to the Sleep mode, but without an active analysis, it can't do so. Thus, when in sleep mode, the computer loses the communication between Clarity and the A/D converter and/or hardware key, and Clarity switches to the Demo mode, destroying the configuration. Backup configuration must be used than.

To solve the problem: All data, such as methods, sequences, data files, calibrations etc. are saved on demand, and are not corrupted when simmilar situation arises. On the other hand, the clarity.cfg file holds the information on the path to these working directories (if set in the Directories dialog accessible via the System - Directories command from the main Clarity window). It is thus necessary to set these directories or select the project that was used before once more on each Clarity Instrument. Unfortunately, the clarity.cfg file is corrupted and the System Configuration settings are lost, so they must be set in the System Configuration dialog manually once more. To repair the damage, follow this process:

Open Clarity and ensure that you are not in the DEMO mode (there would be Clarity DEMO written in the heading of the main Clarity window). If you are in the Demo, download full version from our download section and enter the correctUser code.

Open the System Configuration dialog and configure your system manually (eg. add detectors, LC's, GC's, valves and so on to the configuration, fill in their settings as desired, and distribute them to particular instrument, as intended.

Close the System Configuration dialog and exit the station. The clarity.cfg file was now saved with the correct settings of the configuration.

Open the Clarity once more.

If you had the Directories dialog set before, use the System - Directories command from the Clarity window to set it once more. Then, close the dialog.

Open the Instrument. You might get the information similar to "the current method was prepared on different configuration. Some parametres will be used in default format", if you opened and then saved the method after the clarity.cfg file was corrupted.

Load the desired project to the Instrument; Default clarity.cfg file has Work1 directory set as the project directory, you have, most probably, created your own project before the shutdown. Use the File - Project command, select the appropriate project from the list and press the Open button.

The station should now be in the configuration as before the fall. If the method was opened and saved after the fall of the configuration, there might be necessary to check/set some parametres, mainly on the Method Setup - Acquisition and Method Setup - Measurement tabs (as the demo mode resets the settings of detectors and removes them from the configuration).To prevent from happening this in future: supposing that the cause of the problem was really the sleep mode of the operation system, switch it off according to the following procedure:

In windows XP, use the Start menu and open the Control Pannels. There select the Power Options icon (you may have to switch to the Classic view).

Set the System standby and System hibernates options to Never (as shown in the picture).

Apply changes and use OK to exit this dialog.

The corruption should be prevented for the future. Of course, if it was caused by another reason, such as instabilities in the power network, only good stabilized backup power source may help.

If you add a User Column both to the Summary and Result Table containing the same formula, often you cannot get the same results. In Summary Table you cannot use the First, Last, etc. functions from Special Values. For example "[Reten. Time]first/[Reten. Time]" will not work here. But you can use figures working with the compound itself, for example "[End Time]-[Start Time]".

It is possible to schedule a task which will run Clarity with defined parameters automatically starting a sequence. Proceed as follows:

Prepare a batch file (clarity.bat) to perform the required tasks using the command line parameters:

The batch should contain the following line (example): start C:Clarity_Demo_304Clarity.exe i=2 u="Administrator" psw="" seq=C:Clarity_Demo_304FCFC3.seq run_seq=2

Explanations:

start C:Clarity.exe will start the Clarity in specified directory

i=2 will open the desired instrument (2)

u="Administrator" psw="" will open it as a specified user with specified password (essential, otherwise it stay waiting for this input)

seq=C:Clarity_Demo_304FCFC3.seq specifies the sequence to run

run_seq=2 starts the sequence on instrument 2

Prepare the sequence to be started.

The sequence can contain just one line with the Start up method, or some standards/samples can be defined in the following rows. In the start up method, define to switch the lamp on and flush the system as required to equilibrate.

Use the Task Scheduler

Set the clarity.bat to be started at defined time and date The Scheduler is located in Windows Start menu, Programs, Acessories, System Tools, Scheduled Tasks. Use the advanced properties of the task to fine tune the scheduling

Set the task to be started when you are logged on only and when leaving the PC, do not log yourself off. Remember, there must not run Windows Update which may log you out and restart the PC.

When in Overlay mode one of Move, Scale or 3D View commands is used, all the information about retention times, height and area of peaks are not displayed (as there will be mismatch between result table and the displayed chromatogram). Chromatogram modified by this types of commands could be saved using the Chromatogram - Overlay - Mathematics - Copy command and evaluated or the axes Offset and Scale need to be restored to original values.

Normally, the Active Sequence sends a command to the sampler (over serial line or by digital output) and waits for the start signal from the detector (again over the communication line or digital input). The digital input and output used for this are specified in the Clarity Configuration - Ext. Start Dig. Input (digital input) and Ready Dig. Output (digital output).

In case the injection is performed by some controlled valve or instrument (typically EAS analyzers) not supporting the Injection marker by digital output, the common solution when using DataApex A/D board is to interconnect the digital output set for Ready Out signal directly to the digital input set for Start In command. The digital input on the instrument starting the next run will be connected in parallel. With controlled valve, the injection is then performed during the actual run by switching the valve (or valves) from Clarity Event Table.

In case no A/D board is used and the devices are not offering those digital inputs and outputs (for example with Agilent GC 5890), the suggested workaround will be to use the DataApex Virtual Digital Input Output Loop (auxiliary device, requires A24 LC or A23 GC Control license) to simulate the input/output needed - (those are virtually interconnected).

Yes, but the sequence allows the chromatograms to be stored only in the subdirectories of current project directory. The subdirectories need to be created using an external file manager (e.g. Windows Explorer) before it can be used in Clarity. The path will be specified in the File Name column as a relative path only, i.e for C:\Clarity\Work1\Data\MyProject\ChromatogramName you have to set the filename as MyPyproject\ChromatogramName.

This limitation is necessary to allow the opening chromatograms from sequence and to perform complete reprocess of the sequence from the Batch dialog accessible using the Analysis - Batch command from the Instrument window.

When Clarity cannot find the device's kernel driver (*.sys file). Try to reinstall the drivers. Follow instructions in the Troubleshooting section how to reinstall the device of the respective hardware's manual.

When the device is configured in Clarity but it cannot be found it is inserted to the mainboard's PCI port. Check, whether the card is correctly inserted. Also the card can be nonfunctional.

Cannot load device driver

Probably the card (Int7, Int9, ...) isn't located in the PC or is incorrectly inserted into the PCI port.

Cannot find first board

One of the A/D cards (Int7, Int9, ...) A/D converters didn't pass the test. The card is probably broken.

Cannot find second board

You tried to add to Clarity Configuration second Int7/Int9 board, but in your PC is located only one card. If you have two cards, check, whether are both of the correctly inserted into the PCI port.

Board malfunction

The A/D card in the PC is inserted correctly, but it didn't pass the test of the device's A/D converters chips. Probably the card is broken or the PC is overloaded by other programs activity.

Incompatible device driver

Very rare situation, when there is incompatibility in the device's kernel driver (.sys file) and the Clarity module (.dll file). Follow instructions in the Troubleshooting section how to reinstall the device of the respective hardware's manual.

UPAD device malfunction, NetPAD Device Malfunction

When connected to the PC, the U-PAD or U-PAD2 didn't pass the test of it's A/D converters. Probably the card is broken or the PC is overloaded by other programs activity.

LAN communication

General issues

For LAN communication, one of the 1100/1200 modules must be equipped with a LAN communication card inserted in the MIO slot on the back side of the module (do not mistake it for the CAN connectors used for the internal system communication, using the same RJ45 connectors).

In case you want to use J4100A JetDirect card (alternative to HP JetDirect Print Servers 600N/400N/500X/300X) we don't support it and don't guarantee the functionality.

Connecting single PC directly with 1100/1200 system

In case you need to connect the PC directly with the 1100/1200 system using LAN card, see the chapter 3.3.4 Single PC & network connection in the Agilent 1100 manual.

GPIB Communication

Communication using GP-IB card could not be established

When the communication with the Agilent 1100/1200 system by the GP-IB card could not be established, even if all the parameters are set correctly and the Agilent IO Libraries report the module as connected on the used ID address, then it is necessary to check the Agilent IO Libraries.

The Agilent IO Libraries must be closed (Use the Exit command) before the communication with Clarity can be established.

During the installation of the Agilent IO Libraries, they are added to the programs to be started automaticaly at the system start. It is necessary to remove them from the Windows Start menu, Programs, Startup group because they could not run simultaneously with Clarity.

After the communication was lost, it could not be reestablished

When using the GP-IB USB converter, it may be necessary to disconnect the converter from PC to clear the communication buffers. As the USB can be powered even during computer shutdown, the shutdown and restart may not help.

Yes, from Clarity ver. 3.0 you can add a User Column which display RRT according to a Compound Name. To do this, follow the instructions:

In the Chromatogram, you need a defined peak name from Calibration Table which will be used for calculation of other peaks RRT. Alternatively you can name a peak directly in the chromatogram by using the Force Peak Name function.

In the Result Table of the Chromatogram window, add new User Column and in the Expression field, add [Reten. Time]/[COMPOUNDNAME$Reten. Time], where COMPOUNDNAME is the Compound which will be used as reference peak to calculate the retention times. You can generate the calculation by choosing the Reten. Time in the Columns field, then the "/" sign, and for last, click the Special Values button and click on the Comnpound item. Type name of the column in the Title field and hit OK. New column appear in the Result Table containing the calculated RRT. See the image below.

Yes, it is possible. The function that does so is the same as for adding a new peak - Add Positive. Select the Add Positive function, choose the part of the unresolved peak which you want to split off and add the interval markers to the borders of the new peak. Both peaks will be separated by a vertical line now. Including the current peak's maximum in the interval would produce no result.

This mostly happens on black and white printers which falsely informs Windows that they are color printers. In Report Setup Instrument window - Page Setup tab, check the Black and White Print option. Then all the printed text should be visible.

In case the computer is connected to the Internet, just select the menu Help - Check for Updates in the Clarity main window. New version will be offered. You may need to fill in the registration form and proceed with selecting the default options suggested. Please note, a window requiring computer restart may pop up during the installation, select no and proceed with installation until finished.

Most chromatography systems use a proprietary data format (the main reason is belief that it ensures data integrity for GLP-related requirements). To open and process such chromatograms in Clarity, they must be first exported from the original software in a suitable format. Most commonly used is the AIA (.cdf files) or ASCII (.csv, *.txt, *.asc and other files) formats.

Clarity can import such a files (only the chromatogram data, not integration method or result tables) and process them using the current instrument method.

Chemstation

The export is available with full menus active in Data Analysis view, menu File, command Export file, AIA file....). Due to the way the Chemstation exports the files (they are always named signal01.cdf and stored in user named folders, batch export is not supported), processing is not very convenient and will be quite laborious for a large number of files.

The export of DAD data is even more complicated if not impossible (you will have to export each wavelength separately and combine them to the format which can be imported to Clarity).

EZ Chrom

The chromatograms can be exported during processing, in the Advanced Method Options, Export tab for option Chromatogram the AIA and ASCII formats can be selected.

The ASCII *.asc file format is supported by Clarity both for chromatograms and 3D data. AIA files can be used as well.

These problems may occur during the Setup of an Hardware (Int7, Int9, U-PAD2, ...) in the Clarity Configuration.

Error on setup

Problems on a low level, either a kernel driver or hardware itself.

Can't create ... (device name)

Usually a problem with the control module library.

The *.dll file is either:

not registered,

not compatible with the current cswext.dll,

registered in a different directory and thus using a different cswext.dllversion than the Clarity.exe.

Solution

Uninstall the previous version and then install Clarity again. This usually helps. Follow the chapter for reinstallation in the device's manual. Alternatively it is possible to register the corresponding *.dll file using the Windowssystem32resvr3.exe program.

Yes, Clarity can be connected to any LIMS using the import/export of text files. Results can be exported in various formats to the LIMS and the sample info can be imported from a TXT file into Clarity Sequence which you intend to process.

Yes, Calibration Bracketing is supported directly in Clarity since version 3.0.

What is bracketing?

The bracketing in calibration is a technique, when samples in a long sequence run are evaluated to standards immediately preceding and immediately following the respective samples. It is used to compensate for instability of detector response during the run, for example typical for electrochemical detectors.

Bracketing in Clarity 3.0 and later

1. In the Method Setup - Calculation, set the name for cloned calibration files used during theCalibration Bracketing.

The field enables the use of any text, however it is recommended to use variables appropriate to the calibration method (Line, Date and Time, ...).

This sets the sequence and calibration to the Calibration Bracketing mode. As every unknown sample series is demarcated by calibration standards and as such uses a single calibration file, calibration will be cloned from the previous calibration clone whenever an unknown sample or blank follows the calibration standard. In a newly cloned calibration file, all responses other than responses of the last series of calibration standards (only those standards that follow the unknown samples) are cleared.

Peak detection algorithm i.e. what will be considered as a peak, peak start and peak end position.

Sample bunching, i.e. how many samples will be summarized as one data point. It can be imagined as a very simple signal filter which makes the signal smoother. The formula is that approximately 30 data points is necessary for peak detection. So for instance if you set PW=1min and Sampling rate is 100 Hz, each series of 200 points will be displayed as one point (60*100/30).

In case you can't find a toolbar button or command you can see, for example, in documentation, click the View - Reset All menu item. All buttons will be reset to their default positions. You can find this function in most Clarity windows where the toolbar buttons are located.

Rarely, if you can't locate the main menu, press Alt-V to display the hidden menu.

For preparative purposes a multiposition valve are frequently used as a simple fraction collector.

Knauer provides dedicated control modules for multiposition valve based fraction collectors, however they are available solely in the ClarityChrom Prep OEM version.

To use valves for this purpose in Clarity, it is necessary usually to combine a two position (three way) valve to perform the Collect/Waste function and a multiposition valve to perform the Next vial function.

Clarity Valve control modules also support the needed Next position command. Using the General Purpose Fraction Collector module (requires A24 LC control module) and one of the controlled selection valves (Upchurch, Vici-Valco or Rheodyne MX II series), the fraction collector can be easily created.

In case a signal in Data Acquisition window and chromatograms is cut below 0 Volts, you probably unchecked the Bipolar option in the Setup dialog of DataApex's converter (INT9, U-PAD, Colibrick...). to fix this, open the Setup dialog of respective converter in the Clarity Configuration and check the Bipolar option again and both positive and negative voltages will be measured.

Because the File Created info in the Windows Explorer or any other file manager program informs when the file was created in the File System and this can be different from data of acquisition (when the chromatogram was saved as new one, rewritten, etc.).

When the Send chromatogram by e-mail, Send Method by email or Send Calibration by email does not work, but the Send Report by email works fine - most probably the problem is in Microsoft Outlook Express, which cannot add locked files as attachment (they are currently open in Clarity). Try to use another Email program (MS Outlook, Thunderbird, The Bat!, Eudora, ...), this error was not found in Outlook Express at this time.

General Clarity Limitations

Installation to program files: In Windows Vista or 7, the folder Program files is protected, however Clarity needs user access to the data and system files. It is not recommended to install Clarity there.

Clarity must be at least version 3.0 or later.

DataApex Hardware

U-PAD1 and CB20 board are not supported on 64 bit systems.

INT9 does not work properly on some computers after waking PC up from sleep. It seems to work (no error message) but it gives no data. Solution - to disable and then enable INT9 in the Device Manager.

Control Modules and Tools

User Account Control (UAC) needs to be disabled during installation of some control modules (CTC PAL, Shimadzu LC systems)

To install the CTC PAL autosampler or Shimadzu LC-10/20 system it is necessary to disable the UAC (User Account Control) during installation, otherwise it will be unsuccessful. Similar problems were reported for installation of the Agilent 1100 system, again the UAC disabling helped.

Gilson pump control

Currently the GSIOC driver compatible with Windows Vista is not available, the control of Gilson pumps is thus not possible in this operating system.

Hitachi LaChrom Elite

Problems with detecting the.LaChrom Elite system were observed on Windows Vista and Windows 7 - attributed to the Hitachi driver

Registration of files in Windows Vista or 7

If you manually copy a control module DLL (i.e. not using an installer) you have to run the regsvr32.exe with administrator rights (select Program files, Accessories, Command prompt, right click to open menu, select Run as administrator and type the respective command line, i.e. regsvr32.exe and path to the dll), otherwise error message with code 0x8002801c will appear.

See also Table of compatible Windows OS, Clarity SW and our Hardware

Most probably you need appropriate new User Code (u/c) only. Hardware key (dongle) keeps basic serial number XX-YYYY only and all information about valid version, number of instruments, extensions and control modules are part of User Code.

Recently, during installation on Windows 7 on some computers, the driver pre-installation fails and when Clarity starts, "Incompatible Device Driver" INT7/INT9 is reported. Similar situation may occur for example when the INT7 or INT9 board is inserted into PC before the Clarity and drivers are installed.

C:\Clarity\Clarity.cfg This file stores besides the hardware configuration information also information about the last user logged to a specific instrument and the custom instrument pictures used in the Main window.

C:\Clarity\*.dsk These files store the information about the last used project *.prj and the individual user preferences (windows configurations and layout, tables and graph preferences, user columns etc.). The Clarity.dsk file from the PGM subfolder on the installation CD is copied during installation and used as a template for the *.dsk files of newly created users.

C:\ClarityProjects\*.prj This file stores the info about the project subdirectories (the project directory has the same name as the project *.prj file) and the last used method, sequence, SST method and chromatograms.

C:\ClarityProjects\Clarity.psw In this file the list of users and access rights are saved.

C:\ClarityProjects\Clarity.sno This file contains the User Code.

The information about report setup, window layout, user columns and some other parameters for individual windows and instruments is stored for each user in the respective *.dsk file. Those parameters are not linked to specific methods or projects. Custom instrument picture are placed in the Images subfolder on the installation CD. The new sequence and calibration files are created for the respective template files stored in the Common folder, only when not found there, the program defaults will be usedDefault Report styles are stored in the Common folder, each windows remembers the last used report style, this info is stored in the user *.dsk file.

Analog input cables for Dataapex A/D cards

Recommended maximum lenght is 10 m.

Up to 30 m were used in some cases, however some signal loss or interferences could not be exluded.

RS-232 serial communication cables

The maximum cable lenght depends mainly on the cable quality and a baud rate used. Fairly long cables can be used for baud rates 9600 or less, for 19200 baud a maximum of 15 m is recommended and the lenght will decrease rapidly with a baud rate used.

LAN cables

Yes, using the Snapshot button accessible from Data Acquisition, Analysis or Sequence windows. Remember, the snapshot chromatogram is automatically overwritten by the one from the finished analysis. To keep this snapshot, Save As under a new filename.

Command Export Data exports Result or Summary Tables, chosen Method Parameters and Chromatogram's header eventually Chromatogram data into various file formats, including MS Excel. What parameters to export you can select in the Export Data dialog. Use this function if you want to process the measured data/parameters from the chromatogram in database, spreadsheet or LIMS application.

Command Export Chromatogram exports the measured chromatogram in TXT or AIA format. Use this function, if you want to open and process the chromatogram itself in another Chromatography Datastation application.

If you use Clarity 2.7 and later, use Launch Manager - utility which is a part of the installation. See Clarity Help for more information. If you use an older version of Clarity, the best option is to upgrade to the latest version.

Optionally you can start Clarity using different shortcuts with specific command line parameters for each configuration. Each configuration is stored in separate *.cfg file and Clarity command line parameter sets the name of the corresponding configuration file. See Clarity Help. But remember, this is what the Launch Manager do including other useful features.

The recommended procedure for H53 method integration in Clarity:

use the same Peak Width and Threshold as in standard integration. Do not attempt to increase the Peak Width - this parameter causes a bunching of data as a side effect.

apply Baseline - Together to the whole chromatogram

apply Baseline - Forward Horizontal to the whole chromatogram

mark all the peaks between C10 and C40 as a group (the group boundary lines may exceed into the C10 and C40 peaks, only fully contained peaks will be included)

amend the peak starts and ends by manual peak tools if necessary for the C10 and C40 (use the Peak - Both, with the A time corresponding to the respective C10 or C40 time and B time positive or negative respectively. The times are relative, i.e. will be shifted accordingly in other chromatograms).

create calibration file for C10, C40 and Group A peaks.

To subtract a baseline, in the Method Setup - Advanced dialog, set the baseline chromatogram and in the Matching set No Change. The baseline file should be acquired on stabilized system and preferably without injection of solvent or at least with lower volume of the solvent - otherwise negative artifacts will appear, which will interfere with the correct baseline setting in Clarity.

There is a condition that must be met:

The drawn baseline must not cross the chromatogram line (the negative areas arising do not have any physical meaning)

When the chromatogram is integrated appropriately, use the Method - Save as Template command from the Chromatogram window to save the method as a template method, thus it can be opened on Instrument and used for further measurements.

So there might be a significant difference between analogue and digital signal quality. It depends on many factors like:

Quality of detector D/A converter (analog output resolution may be worse than digital).

Length and quality of analogue cable.

Proper cable connection (symmetrical, non-symmetrical).

Absolute level of analogue signal (lower signal is more influenced by interferences from other laboratory devices).

Proper A/D converted voltage range set (most typical problem is that a detector maximum signal is 10-100 mV only and U-PAD2 voltage range is set to 10 V. This leads to decrease of the voltage step resolution by 100-1000x!

The Sample Rate need to be set to provide enough points to adequately describe the peaks of interest. Recomended is at least 30 points per the narrowest peak width. The default 10 Hz (for DataApex A/D boards) is suitable for most HPLC and packed column GC applications, the capillary GC and CE applications may need higher sample rates.

Yes, the total number of channels per one Instrument in Clarity is 32. In addition, if you have multiple A/D cards and U-PADs/Colibricks connected to PC, their channels can be combined variously on Clarity Instruments. The only limitation of maximum A/D cards and U-PADs/Colibricks depends on your PC's performance. See also examples of Clarity configurations.

When running Clarity on very slow PC or laptop, we can recommend some tips which can improve the Clarity' speed in certain situations: 1) Set the appropriate treshold. 2) Set the appropriate frequency of data acquisition. 3) Turn off the unused tables in Clarity (Performance, SST). 4) Turn off the Overlay function during the Sequence. 5) Turn off the PostRun Printing. 6) In your antivirus SW, turn off the option "Check Files at Change", especially for files used by Clarity (*.raw and *.audit).

The minimum Clarity's hardware requirements can be found at Compatibility page. Very helpful is often to increase the memory in the PC (RAM) rather then improve processor (CPU) speed.

Yes. Normalized % calculation is available in Clarity since version 3.0. Use the NORM option in the Calculation tab of the Method Setup window. With this option set, Clarity automatically verifies:

Sample Amount=0.

All peaks in chromatogram are identified (calibrated).

All peaks in calibration are also identified in the chromatogram.

In older versions of Clarity, use the Amount % column in the Chromatogram - Results table to get the Normalized % calculation. To get correct results, the user must ensure, that all peaks in the chromatogram are identified and calibrated. Remember that Clarity can be updated to a newer version free of charge.

Symptoms

U-PAD2 with Windows 2000 will crash computer, when disconnected during analysis

Cause

There is a bug in the SiLib.sys file (a driver from Silabs) causing a crash of a computer when the hardware is disconnected during an operation. This bug will be probrably not fixed at Silabs, so we recommend to use newer version of Windows (XP, 7, ...) where this problem doesn't occur.

Agilent & HP Chemstation requires for import AIA files which are integrated (must have at least one integrated peak otherwise the import will not be performed), but not calibrated (set calculation to UNCAL before export, otherwise some of the released Chemstation versions may crash during import of such a file.)

The Event Table (especially the Output column) may be corrupted after changes in the instruments' configuration used in it or after some changes in PC's hardware. In such case, it is neccessary to adjust the Event Table.

The SST (System Suitability Test) module is dedicated to calculating of statistical parameters. This module is integrated in the Chromatogram window. This module can be purchased additionaly and is available as part number (p/n) A22.

There may be an error message hidden behind the splashscreen (picture). You can use the following workaround:Start the station with a parameter -hide_splash, this should reveal the problem.

The easiest way is to modify the shortcut icon on the desktop - right mouse click on the icon to enter its properties page and add this parameter after the "c:clarity liteclarity.exe" in the Target field.

If the problem persists, update Clarity to the newest version or contact your local distributor.

Find out what instruments (detectors, autosamplers, ...) are you using in your laboratory and what do you want to connect to Clarity. Contact one of our distributors or email us directly to sales@dataapex.com.

Our current INT9, U-PAD2 and Colibrick A/D converters can acquire data at the maximum frequency 400 Hz, that means 400 samples per second. This frequency can be set up in the software. The older INT7 and U-PAD1 A/D converters can acquire data at the maximum frequency 100 Hz.

A slowdown in the computer performance after installing the drivers for the Sentinel protective key may be caused by incorrect settings selected during the installation. These problems occur when Clarity is running and you try to work with files/directories on the network (for example, searching for the network printer). Clarity installer correctly installs Sentinel drivers with disabled "Sentinel protection server" and "Sentinel Keys Server" options. However, if the drivers were previously installed manually, the options that cause the slowdown could have been set.

Solution:

Run the Sentinel Protection Installer 7.3.2.exe program found in the HW_DRIVERSSENTINEL subdirectory on your Clarity CD

Get to the "Custom Setup" dialog: - If Sentinel drivers are already installed on your computer, choose the "Modify" option in the first dialog. - In case you have no Sentinel drivers installed on your computer so far, select the "Custom installation" option during the installation.

In the list of installed devices, disable the “Sentinel Protection Server” and “Sentinel Keys Server” options.

While installing Clarity version 2.5 on a PC with Windows Vista, where Clarity older than version 2.4.4.124 was previously installed, follow these steps:

Remove your protective key (Rockey or Sentinel).

In case of Rockey key, manually delete files rockey4.sys and rockey4usb.sys from the SYSTEM32DRIVERS subdirectory of your main Windows directory.

Restart your computer.

Uninstall the driver using the InstDrv.exe (in case of Rockey) program found in the HW_DRIVERSROCKEY subdirectory or Sentinel Protection Installer 7.3.2.exe (in case of Sentinel) program found in the HW_DRIVERSSENTINEL subdirectory on your Clarity CD.

Restart your computer.

Install the drivers by the same program (InstDrv.exe or Sentinel Protection Installer 7.3.2.exe, respectively).

Insert the protective key.

If you won’t follow these instructions, the crash of the system may happen. This is caused by persisting versions of Vista-incompatible Sentinel or Rockey drivers. To remedy possible problems, re-install the drivers according to the instructions given above. Also, crash of Windows Vista may occur when the Rockey protective key is removed after an older version of Clarity was replaced by version 2.5. Again, in order to repair the trouble caused, do not insert the Rockey protective key back to the system and re-install the drivers as shown above.

a) update Clarity software

If you have Clarity 2.3 and older - download the latest 2.3.x version from CLARITY PREVIOUS FULL VERSIONS section (update from this version to Clarity 2.4 and later would require to purchase HW Key (p/n C550) for manipulation fee.

If you have Clarity 2.4. and later - download the latest available version from CLARITY FULL VERSIONS section

Disconnect the U-PAD before installing the update.

The uninstallation of earlier version is also strongly recommended - use the Remove Clarity command from the Windows Start menu, Programs, Clarity program Group. This will remove the program components only, leaving your configuration and datafiles intact.

This happens usually when upgrading Clarity from earlier version. To get Passed for IQ result, it is necessary to remove the previous Clarity installation first using the "Remove" command from the Windows Start menu, Programs - Clarity program group. The IQ program checks all registered files and in case they are no more used in the new version, they will cause the check to fail. However, the station will usually function correctly. The Remove command will remove the program files only, leaving the configuration and data intact.

Clarity EVAL was renamed to Clarity Offline. It is because users often misinterpreted Clarity EVAL for a demo version of Clarity software. Since it is a full featured product intended for working with data and preparing methods without the possibility to acquire data, the name "Clarity Offline" better reflects its purpose.

It is not possible to use them simultaneously. However it is possible to install both versions on the same computer and start them by a start_clarity.bat file. This bat file will re-register the dynamically linked libraries to the proper version. You can download the Clarity-multiple-instances-on-a-single-computer.zip file with the start_clarity.bat and detailed description on how to use it.

N/A means not available, the Result table will display this when the computation does not make sense. For example if a calibration curve does not pass through zero, it can produce negative amount for given response, this is of course nonsense. Correcting the calibration curve fit will most probably fix this problem.

It is not posible even technically for the device to run on two independent timebases. This problem applies generally to all Control modules. Some devices contain parts "subdevices", such as Signals in FLD that cannot cannot be used on two independent chromatography sets at once. It is usually not technically possible. The most recent Control modules will show a warning during the configuration procedure when you attempt to split indivisible device between multiple Clarity Instruments.

Yes, it can, however the philosophy of use is slightly different. The peak areas belonging to a selected group of peaks are summed and the group can be named and calibrated as a single compound. Please, see the corresponding parts of Reference and User guides. Especially in the calculation of Result table Total line and Amount % column are some potential problems, if the calculation procedure is not understood.

The overlay (Menu File, command Overlay mode) must be On to display several chromatograms simultaneously. The printing of chromatograms in overlay is governed by the options "Tilled by" selected in the Report setup, section Chromatogram. The options are Signals (each signal will be printed in separate box), Chromatogram (signals from one chromatogram only are overlaid, each chromatogram is printed in separate box), Not tilled (the overlayed chromatograms are printed as seen on screen).

A new project can be created (opened, changed..) in the current instrument directory only. However an arbitrary directory for each instrument can be set in the main Clarity window using the System - Directory command.

The corresponding instrument displays only the simulated curve or has a so-called DEMO driver attached instead of the data acquisition driver. Meaning that the signal is not real but simulated from a data file. Reason for the watermark "Simulated" could be one of the following:

Either you have a demo detector allocated on that instrument. Check your configuration, remove the demo detector and allocate an A/D converter.

You migh have installed DEMO version which does not allow real time acquisition. Navigate to our download section and download a full version. Note that you will need to insert a correct User code, otherwise Clarity will not start up.

Yes, we will continue to provide updates free of charge. The latest version of our software is available from our web page in the download section. Users can also automatically update SW directly from their Clarity software, using the Check for update command.

Yes, upgrades are available. If users wish to upgrade to Clarity they have to buy an upgrade according to the current pricelist. Have a look in the Product catalog, the upgrade options are listed there.

Users can load CSW32 files into Clarity software. The Save command automatically converts CSW32 data to the new “Clarity format”.

However, because of the new multi-detector measurement feature, users will need to edit the CSW32 method/calibration files in case he/she has an instrument with more than 1 detector. CSW32 uses a separate method for every detector. Clarity uses one method for the entire Instrument with up to four detectors. For further details please refer to “Clarity vs. CSW32 Guide”.